Officers were ready and waiting – and had stopped trains – after learning of a planned clash between two groups in the vicinity of the station and Federation Square at 11.50pm on Saturday.

A drunken melee broke out in Swanston Street just outside the station about six minutes later.

Three men aged in their 20s were arrested and at least one man was injured in the drunken fight, which is believed to have involved about 30 young men.

A number of smaller scuffles were also quelled, including a brawl that erupted on platforms four and five, raising fears of someone falling onto train tracks.

Melbourne East area commander Inspector Trevor Cornwill said police had stopped the trains before the first brawl started.

He said they had learnt of the "organised" encounter earlier in the night. He wouldn't say how, or exactly when, but police had "ample time to deploy resources".

He said the information gave police time to send officers – reportedly up to 100 – from transit, rostered city and the mounted branch to the scene to handle the incident.

Police drew their batons and used capsicum spray to disperse the group within minutes.

"Last night police became aware that there was a planned gathering of a couple of groups of people in the city," Inspector Cornwill said. "It [was] proposed that they become involved in a fight outside Flinders Street Station or Federation Square.

"We were told that that would occur about 10 minutes to midnight, so we put our resources that we had on in the city at that location.

"And a fight did erupt about four minutes to midnight. Police quickly intervened to stop that fight. It then broke off into a number of small scuffles through Flinders Street Station, and police were also able to break up those fights very quickly."

Inspector Cornwill said the reason for the brawl was not yet known.

Those arrested were a man in his 20s from Reservoir, and two men, also in their 20s, from Westmeadows. No weapons were found at the scene.

The men were interviewed and would be charged on summons in relation to "assault, behavioural and alcohol offences".

Inspector Cornwill said no known groups were involved beyond youths in their early 20s.

Police would review CCTV and other city camera footage to try to identify who was involved. Inspector Cornwill called on members of the public to supply any footage from their phones to Crime Stoppers.

He said police had found out about the brawl "through a number of sources. We can't go into those sources, about how we found out, but certainly it was accurate and gave us an indication of the time the fight would occur.

"As a precautionary measure, when we knew there was going to be an organised fight at the train station, we stopped trains, only for approximately five minutes, while police responded to the event, just as a safety precaution to make sure no one was injured falling from any platforms."

A man in his 40s, who is believed to have received head injuries, was taken to St Vincent's Hospital in a stable condition by paramedics about 1am.

A second man was found later, at 2.15am, also with head injuries. He was taken to the Royal Melbourne Hospital in a stable condition, but it was not clear whether the man's injuries related to the brawl.

Inspector Cornwill said there had been no reported injuries to police or members of the public.

He said it was "deplorable" that youths were planning fights at the city's major train station.

"Certainly, deplorable behaviour by people involved in the fight," he said. "You've got people in the city at this time of year attending social functions, shopping, out enjoying the late-night entertainment."

He said the behaviour wouldn't "be tolerated in our society".

"It's not part of our society, it's not who we are as a society of people, and certainly police will act on any brawls that occur," he said.

He said there could have been more injuries to those involved, "but certainly the police response was very swift and quick, which prevented those injuries occurring".